Introduction: LIH Department DII

Here are preliminary results of the bibliometric mapping of the 2022 Luxembourg research evaluation. Its purpose is:

The method for the research-field-mapping can be reviewed here:

Rakas, M., & Hain, D. S. (2019). The state of innovation system research: What happens beneath the surface?. Research Policy, 48(9), 103787.

Seed Articles

The seed articles deemed representative for the active areas of research in the institution, and include authors affiliated with the institution. They can be selected in three ways:

  1. Via bibliographic clustering of the institutions publications and selection of most central articles per cluster (only clsuters where n >= 0.05N). Selection can be found at: https://github.com/daniel-hain/biblio_lux_2022/blob/master/output/seed/scopus_lih_dii_seed.csv
  2. Manual selection of relevant publications.
  3. A combination of 1. and 2.

The present analysis is based on the following seed articles:

AU PY TI JI
SZPAKOWSKA M;DECKER AM;MEYR… 2021 THE NATURAL ANALGESIC CONOLIDINE TARGETS THE NEWLY IDENTIFIED OPIOID SCAVENGER ACKR3/CXCR7 SIGNAL TRANSDUCT. TARGET. T…
GOLEBSKI K;LAYHADI JA;SAHIN… 2021 INDUCTION OF IL-10-PRODUCING TYPE 2 INNATE LYMPHOID CELLS BY ALLERGEN IMMUNOTHERAPY IS ASSOCIATED… IMMUNITY
MEYRATH M;SZPAKOWSKA M;ZEIN… 2020 THE ATYPICAL CHEMOKINE RECEPTOR ACKR3/CXCR7 IS A BROAD-SPECTRUM SCAVENGER FOR OPIOID PEPTIDES NAT. COMMUN.
KURNIAWAN H;FRANCHINA DG;GU… 2020 GLUTATHIONE RESTRICTS SERINE METABOLISM TO PRESERVE REGULATORY T CELL FUNCTION CELL METAB.
MARTENS EC;NEUMANN M;DESAI MS 2018 INTERACTIONS OF COMMENSAL AND PATHOGENIC MICROORGANISMS WITH THE INTESTINAL MUCOSAL BARRIER NAT. REV. MICROBIOL.

Topic modelling

Here, we report the results of a LDA topic-modelling (basically, clustering on words) on all title+abstract texts.

Topics by topwords

Note: While this static vies is helpful, I recommend using the interactive LDAVis version to be found under https://daniel-hain.github.io/biblio_lux_2022/output/topic_modelling/LDAviz_lih_dii.rds/index.html#topic=1&lambda=0.60&term=. For functionality and usage, see technical description in the next tab.

Topics over time

Technical Description

LDA Topic Modelling

Topic modeling is a type of statistical modeling for discovering the abstract “topics” that occur in a collection of documents. Latent Dirichlet Allocation (LDA, Blei et al., 2003) is an example of topic model and is used to classify text in a document to a particular topic.

LDA is a generative probabilistic model that assumes each topic is a mixture over an underlying set of words, and each document is a mixture of over a set of topic probabilities. It builds a topic per document model and words per topic model, modeled as Dirichlet distributions.

LDAVis

LDAvis is a web-based interactive visualisation of topics estimated using LDA (Sievert & Shirley, 2014). It provides a global view of the topics (and how they differ from each other), while at the same time allowing for a deep inspection of the terms most highly associated with each individual topic. The package extracts information from a fitted LDA topic model to inform an interactive web-based visualization. The visualisation has two basic pieces.

The left panel visualise the topics as circles in the two-dimensional plane whose centres are determined by computing the Jensen–Shannon divergence between topics, and then by using multidimensional scaling to project the inter-topic distances onto two dimensions. Each topic’s overall prevalence is encoded using the areas of the circles.

The right panel depicts a horizontal bar chart whose bars represent the individual terms that are the most useful for interpreting the currently selected topic on the left. A pair of overlaid bars represent both the corpus-wide frequency of a given term as well as the topic-specific frequency of the term.

The \(\lambda\) slider allows to rank the terms according to term relevance. By default, the terms of a topic are ranked in decreasing order according their topic-specific probability ( \(\lambda\) = 1 ). Moving the slider allows to adjust the rank of terms based on much discriminatory (or “relevant”) are for the specific topic. The suggested optimal value of \(\lambda\) is 0.6.

Knowledge Bases: Co-Citation network analysis

Note: This analysis refers the co-citation analysis, where the cited references and not the original publications are the unit of analysis. See tab Technical descriptionfor additional explanations

Knowledge Bases summary

In order to partition networks into components or clusters, we deploy a community detection technique based on the Lovain Algorithm (Blondel et al., 2008). The Lovain Algorithm is a heuristic method that attempts to optimize the modularity of communities within a network by maximizing within- and minimizing between-community connectivity. We identify the following communities = knowledge bases.

name dgr_int dgr
Knowledge Base 1: KB 1: unlabeled (n = 2515, density =2.12)
MARTENS E.C. CHIANG H.C. GORDON J.I. MUCOSAL GLYCAN FORAGING ENHANCES FITNESS AND TRANSMISSION OF A SACCHAROLYTIC HUMAN GUT BACTERIAL SYMBIONT (2008) 2362 2561
KOROPATKIN N.M. CAMERON E.A. MARTENS E.C. HOW GLYCAN METABOLISM SHAPES THE HUMAN GUT MICROBIOTA (2012) 2306 2537
EL KAOUTARI A. ARMOUGOM F. GORDON J.I. RAOULT D. HENRISSAT B. THE ABUNDANCE AND VARIETY OF CARBOHYDRATE-ACTIVE ENZYMES IN THE HUMAN GUT MICROBIOTA … 1816 1916
JOHANSSON M.E. PHILLIPSON M. PETERSSON J. VELCICH A. HOLM L. HANSSON G.C. THE INNER OF THE TWO MUC2 MUCIN-DEPENDENT MUCUS LAYERS IN COLON IS DEVOID… 1351 1423
SONNENBURG E.D. SMITS S.A. TIKHONOV M. HIGGINBOTTOM S.K. WINGREEN N.S. SONNENBURG J.L. DIET-INDUCED EXTINCTIONS IN THE GUT MICROBIOTA COMPOUND OVER… 1254 1310
TAILFORD L.E. CROST E.H. KAVANAUGH D. JUGE N. MUCIN GLYCAN FORAGING IN THE HUMAN GUT MICROBIOME (2015) 1201 1273
FURUSAWA Y. OBATA Y. FUKUDA S. ENDO T.A. NAKATO G. TAKAHASHI D. COMMENSAL MICROBE-DERIVED BUTYRATE INDUCES THE DIFFERENTIATION OF COLONIC REGULATOR… 1053 1692
ROUND J.L. MAZMANIAN S.K. INDUCIBLE FOXP3+ REGULATORY T-CELL DEVELOPMENT BY A COMMENSAL BACTERIUM OF THE INTESTINAL MICROBIOTA (2010) 1046 1368
KOROPATKIN N.M. MARTENS E.C. GORDON J.I. SMITH T.J. STARCH CATABOLISM BY A PROMINENT HUMAN GUT SYMBIONT IS DIRECTED BY THE RECOGNITION OF AMYLOSE H… 1020 1044
FURUSAWA Y. OBATA Y. FUKUDA S. ENDO T.A. NAKATO G. TAKAHASHI D. NAKANISHI Y. KATO T. COMMENSAL MICROBE-DERIVED BUTYRATE INDUCES THE DIFFERENTIATION… 1006 1093
Knowledge Base 2: KB 2: unlabeled (n = 1515, density =5.23)
MACIVER N.J. MICHALEK R.D. RATHMELL J.C. METABOLIC REGULATION OF T LYMPHOCYTES (2013) 2627 2844
MICHALEK R.D. GERRIETS V.A. JACOBS S.R. MACINTYRE A.N. MACIVER N.J. MASON E.F. SULLIVAN S.A. RATHMELL J.C. CUTTING EDGE: DISTINCT GLYCOLYTIC AND LI… 2223 2499
ZENG H. YANG K. CLOER C. NEALE G. VOGEL P. CHI H. MTORC1 COUPLES IMMUNE SIGNALS AND METABOLIC PROGRAMMING TO ESTABLISH T(REG) 2144 3046
PEARCE E.L. POFFENBERGER M.C. CHANG C.H. JONES R.G. FUELING IMMUNITY: INSIGHTS INTO METABOLISM AND LYMPHOCYTE FUNCTION (2013) 1651 1904
SHI L.Z. WANG R. HUANG G. VOGEL P. NEALE G. GREEN D.R. CHI H. HIF1ALPHA-DEPENDENT GLYCOLYTIC PATHWAY ORCHESTRATES A METABOLIC CHECKPOINT FOR THE DI… 1605 1774
SINCLAIR L.V. ROLF J. EMSLIE E. SHI Y.B. TAYLOR P.M. CANTRELL D.A. CONTROL OF AMINO-ACID TRANSPORT BY ANTIGEN RECEPTORS COORDINATES THE METABOLIC R… 1556 1754
SHI L.Z. WANG R. HUANG G. VOGEL P. NEALE G. GREEN D.R. HIF1ALPHA-DEPENDENT GLYCOLYTIC PATHWAY ORCHESTRATES A METABOLIC CHECKPOINT FOR THE DIFFERENT… 1547 2001
PENG M. YIN N. CHHANGAWALA S. XU K. LESLIE C.S. LI M.O. AEROBIC GLYCOLYSIS PROMOTES T HELPER 1 CELL DIFFERENTIATION THROUGH AN EPIGENETIC MECHANISM… 1501 1650
MICHALEK R.D. GERRIETS V.A. JACOBS S.R. MACINTYRE A.N. MACIVER N.J. MASON E.F. CUTTING EDGE: DISTINCT GLYCOLYTIC AND LIPID OXIDATIVE METABOLIC PROG… 1441 1753
BUCK M.D. O’SULLIVAN D. PEARCE E.L. T CELL METABOLISM DRIVES IMMUNITY (2015) 1397 1538
Knowledge Base 3: KB 3: unlabeled (n = 1400, density =4.88)
HORI S. NOMURA T. SAKAGUCHI S. CONTROL OF REGULATORY T CELL DEVELOPMENT BY THE TRANSCRIPTION FACTOR FOXP3 (2003) 6308 7084
FONTENOT J.D. GAVIN M.A. RUDENSKY A.Y. FOXP3 PROGRAMS THE DEVELOPMENT AND FUNCTION OF CD4+CD25+ REGULATORY T CELLS (2003) 5095 5664
ZHENG Y. JOSEFOWICZ S. CHAUDHRY A. PENG X.P. FORBUSH K. RUDENSKY A.Y. ROLE OF CONSERVED NON-CODING DNA ELEMENTS IN THE FOXP3 GENE IN REGULATORY T-C… 1994 2336
SAKAGUCHI S. SAKAGUCHI N. ASANO M. ITOH M. TODA M. IMMUNOLOGIC SELF-TOLERANCE MAINTAINED BY ACTIVATED T CELLS EXPRESSING IL-2 RECEPTOR ALPHA-CHAINS… 1742 2055
JOSEFOWICZ S.Z. LU L.F. RUDENSKY A.Y. REGULATORY T CELLS: MECHANISMS OF DIFFERENTIATION AND FUNCTION (2012) 1694 2050
KHATTRI R. COX T. YASAYKO S.A. RAMSDELL F. AN ESSENTIAL ROLE FOR SCURFIN IN CD4+CD25+ T REGULATORY CELLS (2003) 1576 1655
SAKAGUCHI S. YAMAGUCHI T. NOMURA T. ONO M. REGULATORY T CELLS AND IMMUNE TOLERANCE (2008) 1407 1575
LI X. LIANG Y. LEBLANC M. BENNER C. ZHENG Y. FUNCTION OF A FOXP3 CIS-ELEMENT IN PROTECTING REGULATORY T CELL IDENTITY (2014) 1192 1329
LEVINE A.G. ARVEY A. JIN W. RUDENSKY A.Y. CONTINUOUS REQUIREMENT FOR THE TCR IN REGULATORY T CELL FUNCTION (2014) 957 1059
FENG Y. ARVEY A. CHINEN T. VAN DER VEEKEN J. GASTEIGER G. RUDENSKY A.Y. CONTROL OF THE INHERITANCE OF REGULATORY T CELL IDENTITY BY A CIS ELEMENT I… 949 1088
Knowledge Base 4: KB 4: unlabeled (n = 1279, density =5.5)
LOCASALE J.W. SERINE GLYCINE AND ONE-CARBON UNITS: CANCER METABOLISM IN FULL CIRCLE (2013) 2513 2619
DUCKER G.S. RABINOWITZ J.D. ONE-CARBON METABOLISM IN HEALTH AND DISEASE (2017) 1728 1793
POSSEMATO R. MARKS K.M. SHAUL Y.D. PACOLD M.E. KIM D. BIRSOY K. SETHUMADHAVAN S. JHA A.K. FUNCTIONAL GENOMICS REVEAL THAT THE SERINE SYNTHESIS PATH… 1661 1718
LOCASALE J.W. GRASSIAN A.R. MELMAN T. LYSSIOTIS C.A. MATTAINI K.R. BASS A.J. HEFFRON G. SHARFI H. PHOSPHOGLYCERATE DEHYDROGENASE DIVERTS GLYCOLYTIC… 1653 1721
FAN J. YE J. KAMPHORST J.J. SHLOMI T. THOMPSON C.B. RABINOWITZ J.D. QUANTITATIVE FLUX ANALYSIS REVEALS FOLATE-DEPENDENT NADPH PRODUCTION (2014) 1503 1568
TIBBETTS A.S. APPLING D.R. COMPARTMENTALIZATION OF MAMMALIAN FOLATE-MEDIATED ONE-CARBON METABOLISM (2010) 1502 1525
MADDOCKS O.D. BERKERS C.R. MASON S.M. ZHENG L. BLYTH K. GOTTLIEB E. VOUSDEN K.H. SERINE STARVATION INDUCES STRESS AND P53-DEPENDENT METABOLIC REMOD… 1336 1370
LABUSCHAGNE C.F. VAN DEN BROEK N.J. MACKAY G.M. VOUSDEN K.H. MADDOCKS O.D. SERINE BUT NOT GLYCINE SUPPORTS ONE-CARBON METABOLISM AND PROLIFERATION … 1257 1278
VANDER HEIDEN M.G. CANTLEY L.C. THOMPSON C.B. UNDERSTANDING THE WARBURG EFFECT: THE METABOLIC REQUIREMENTS OF CELL PROLIFERATION (2009) 1235 2524
YANG M. VOUSDEN K.H. SERINE AND ONE-CARBON METABOLISM IN CANCER (2016) 1233 1298
Knowledge Base 5: KB 5: unlabeled (n = 1238, density =5.87)
COX L. NELSON H. LOCKEY R. CALABRIA C. CHACKO T. FINEGOLD I. ALLERGEN IMMUNOTHERAPY: A PRACTICE PARAMETER THIRD UPDATE (2011) 1118 1124
CANONICA G.W. COX L. PAWANKAR R. SUBLINGUAL IMMUNOTHERAPY: WORLD ALLERGY ORGANIZATION POSITION PAPER 2013 UPDATE (2014) 999 999
AKDIS M. AKDIS C.A. MECHANISMS OF ALLERGEN-SPECIFIC IMMUNOTHERAPY: MULTIPLE SUPPRESSOR FACTORS AT WORK IN IMMUNE TOLERANCE TO ALLERGENS (2014) 945 986
JUTEL M. JAEGER L. SUCK R. MEYER H. FIEBIG H. CROMWELL O. ALLERGEN-SPECIFIC IMMUNOTHERAPY WITH RECOMBINANT GRASS POLLEN ALLERGENS (2005) 916 937
DURHAM S.R. EMMINGER W. KAPP A. SQ-STANDARDIZED SUBLINGUAL GRASS IMMUNOTHERAPY: CONFIRMATION OF DISEASE MODIFICATION 2 YEARS AFTER 3 YEARS OF TREAT… 913 913
CANONICA G.W. COX L. PAWANKAR R. BAENA-CAGNANI C.E. BLAISS M. BONINI S. SUBLINGUAL IMMUNOTHERAPY: WORLD ALLERGY ORGANIZATION POSITION PAPER 2013 UP… 906 906
SHAMJI M.H. DURHAM S.R. MECHANISMS OF ALLERGEN IMMUNOTHERAPY FOR INHALED ALLERGENS AND PREDICTIVE BIOMARKERS (2017) 853 880
DURHAM S.R. EMMINGER W. KAPP A. DE MONCHY J.G. RAK S. SCADDING G.K. SQ-STANDARDIZED SUBLINGUAL GRASS IMMUNOTHERAPY: CONFIRMATION OF DISEASE MODIFIC… 844 847
DURHAM S.R. WALKER S.M. VARGA E.M. LONG-TERM CLINICAL EFFICACY OF GRASS-POLLEN IMMUNOTHERAPY (1999) 840 843
BLAISS M. MALONEY J. NOLTE H. GAWCHIK S. YAO R. SKONER D.P. EFFICACY AND SAFETY OF TIMOTHY GRASS ALLERGY IMMUNOTHERAPY TABLETS IN NORTH AMERICAN CH… 830 830
Knowledge Base 6: KB 6: unlabeled (n = 1137, density =7.84)
GASTEIGER G. FAN X. DIKIY S. LEE S.Y. RUDENSKY A.Y. TISSUE RESIDENCY OF INNATE LYMPHOID CELLS IN LYMPHOID AND NONLYMPHOID ORGANS (2015) 2297 2310
BARTEMES K.R. KEPHART G.M. FOX S.J. KITA H. ENHANCED INNATE TYPE 2 IMMUNE RESPONSE IN PERIPHERAL BLOOD FROM PATIENTS WITH ASTHMA (2014) 1535 1535
SILVER J.S. KEARLEY J. COPENHAVER A.M. SANDEN C. MORI M. YU L. INFLAMMATORY TRIGGERS ASSOCIATED WITH EXACERBATIONS OF COPD ORCHESTRATE PLASTICITY O… 1452 1461
DOHERTY T.A. KHORRAM N. LUND S. MEHTA A.K. CROFT M. BROIDE D.H. LUNG TYPE 2 INNATE LYMPHOID CELLS EXPRESS CYSTEINYL LEUKOTRIENE RECEPTOR 1 WHICH RE… 1210 1210
CONSTANTINIDES M.G. MCDONALD B.D. VERHOEF P.A. BENDELAC A. A COMMITTED PRECURSOR TO INNATE LYMPHOID CELLS (2014) 1206 1210
ARTIS D. SPITS H. THE BIOLOGY OF INNATE LYMPHOID CELLS (2015) 1189 1265
LAO-ARAYA M. STEVELING E. SCADDING G.W. DURHAM S.R. SHAMJI M.H. SEASONAL INCREASES IN PERIPHERAL INNATE LYMPHOID TYPE 2 CELLS ARE INHIBITED BY SUBC… 1118 1606
VIVIER E. ARTIS D. COLONNA M. DIEFENBACH A. DI SANTO J.P. EBERL G. INNATE LYMPHOID CELLS: 10 YEARS ON (2018) 1079 1079
OHNE Y. SILVER J.S. THOMPSON-SNIPES L. COLLET M.A. BLANCK J.P. CANTAREL B.L. IL-1 IS A CRITICAL REGULATOR OF GROUP 2 INNATE LYMPHOID CELL FUNCTION … 918 918
VON MOLTKE J. JI M. LIANG H.E. LOCKSLEY R.M. TUFT-CELL-DERIVED IL-25 REGULATES AN INTESTINAL ILC2-EPITHELIAL RESPONSE CIRCUIT (2016) 911 1254
Knowledge Base 7: KB 7: unlabeled (n = 1055, density =4.15)
LEVOYE A. BALABANIAN K. BALEUX F. BACHELERIE F. LAGANE B. CXCR7 HETERODIMERIZES WITH CXCR4 AND REGULATES CXCL12-MEDIATED G PROTEIN SIGNALING (2009) 2270 2283
LUKER K.E. STEELE J.M. MIHALKO L.A. RAY P. LUKER G.D. CONSTITUTIVE AND CHEMOKINE-DEPENDENT INTERNALIZATION AND RECYCLING OF CXCR7 IN BREAST CANCER … 900 903
ZLOTNIK A. YOSHIE O. THE CHEMOKINE SUPERFAMILY REVISITED (2012) 815 821
BURNS J.M. SUMMERS B.C. WANG Y. MELIKIAN A. BERAHOVICH R. MIAO Z. A NOVEL CHEMOKINE RECEPTOR FOR SDF-1 AND I-TAC INVOLVED IN CELL SURVIVAL CELL ADH… 799 802
DISSOCIATION OF CXCR4 ACTIVATION FROM BINDING AND INHIBITION OF HIV-1 (1997) 754 760
GRIFFITH J.W. SOKOL C.L. LUSTER A.D. CHEMOKINES AND CHEMOKINE RECEPTORS: POSITIONING CELLS FOR HOST DEFENSE AND IMMUNITY (2014) 644 651
KALATSKAYA I. BERCHICHE Y.A. GRAVEL S. LIMBERG B.J. ROSENBAUM J.S. HEVEKER N. AMD3100 IS A CXCR7 LIGAND WITH ALLOSTERIC AGONIST PROPERTIES (2009) 644 644
GRAHAM G.J. LOCATI M. MANTOVANI A. ROT A. THELEN M. THE BIOCHEMISTRY AND BIOLOGY OF THE ATYPICAL CHEMOKINE RECEPTORS (2012) 519 519
ZLOTNIK A. YOSHIE O. CHEMOKINES: A NEW CLASSIFICATION SYSTEM AND THEIR ROLE IN IMMUNITY (2000) 497 497
NAUMANN U. CAMERONI E. PRUENSTER M. MAHABALESHWAR H. RAZ E. ZERWES H.G. ROT A. THELEN M. CXCR7 FUNCTIONS AS A SCAVENGER FOR CXCL12 AND CXCL11 (2010) 475 475
Knowledge Base 8: KB 8: unlabeled (n = 713, density =8.23)
FURUSAWA Y. COMMENSAL MICROBE-DERIVED BUTYRATE INDUCES THE DIFFERENTIATION OF COLONIC REGULATORY T CELLS (2013) 1485 1761
SMITH P.M. THE MICROBIAL METABOLITES SHORT-CHAIN FATTY ACIDS REGULATE COLONIC TREG CELL HOMEOSTASIS (2013) 1095 1276
IVANOV I.I. INDUCTION OF INTESTINAL TH17 CELLS BY SEGMENTED FILAMENTOUS BACTERIA (2009) 989 1111
DAVID L.A. DIET RAPIDLY AND REPRODUCIBLY ALTERS THE HUMAN GUT MICROBIOME (2014) 813 942
ATARASHI K. TREG INDUCTION BY A RATIONALLY SELECTED MIXTURE OF CLOSTRIDIA STRAINS FROM THE HUMAN MICROBIOTA (2013) 765 918
ARPAIA N. METABOLITES PRODUCED BY COMMENSAL BACTERIA PROMOTE PERIPHERAL REGULATORY T-CELL GENERATION (2013) 703 886
ATARASHI K. INDUCTION OF COLONIC REGULATORY T CELLS BY INDIGENOUS CLOSTRIDIUM SPECIES (2011) 670 770
NG K.M. MICROBIOTA-LIBERATED HOST SUGARS FACILITATE POST-ANTIBIOTIC EXPANSION OF ENTERIC PATHOGENS (2013) 640 747
STRUCTURE FUNCTION AND DIVERSITY OF THE HEALTHY HUMAN MICROBIOME (2012) 631 1512
BUFFIE C.G. PRECISION MICROBIOME RECONSTITUTION RESTORES BILE ACID MEDIATED RESISTANCE TO CLOSTRIDIUM DIFFICILE (2015) 574 611
Knowledge Base 9: KB 9: unlabeled (n = 654, density =5.73)
AL-HASANI R. BRUCHAS M.R. MOLECULAR MECHANISMS OF OPIOID RECEPTOR-DEPENDENT SIGNALING AND BEHAVIOR (2011) 409 409
BOHN L.M. GAINETDINOV R.R. LIN F.T. LEFKOWITZ R.J. CARON M.G. MU-OPIOID RECEPTOR DESENSITIZATION BY BETA-ARRESTIN-2 DETERMINES MORPHINE TOLERANCE B… 373 373
BOHN L.M. LEFKOWITZ R.J. GAINETDINOV R.R. PEPPEL K. CARON M.G. LIN F.T. ENHANCED MORPHINE ANALGESIA IN MICE LACKING BETA-ARRESTIN 2 (1999) 358 358
GUREVICH E.V. GUREVICH V.V. ARRESTINS ARE UBIQUITOUS REGULATORS OF CELLULAR SIGNALING PATHWAYS (2006) 324 324
PETERSON Y.K. LUTTRELL L.M. THE DIVERSE ROLES OF ARRESTIN SCAFFOLDS IN G PROTEIN-COUPLED RECEPTOR SIGNALING (2017) 310 310
CARPENTER B. NEHMÉ R. WARNE T. LESLIE A.G. TATE C.G. STRUCTURE OF THE ADENOSINE A(2A) 302 302
SCHMID C.L. KENNEDY N.M. ROSS N.C. LOVELL K.M. YUE Z. MORGENWECK J. CAMERON M.D. BOHN L.M. BIAS FACTOR AND THERAPEUTIC WINDOW CORRELATE TO PREDICT … 295 295
SONG X. COFFA S. FU H. GUREVICH V.V. HOW DOES ARRESTIN ASSEMBLE MAPKS INTO A SIGNALING COMPLEX? (2009) 292 292
INDRISCHEK H. PROHASKA S.J. GUREVICH V.V. GUREVICH E.V. STADLER P.F. UNCOVERING MISSING PIECES: DUPLICATION AND DELETION HISTORY OF ARRESTINS IN DE… 285 285
GUREVICH V.V. GUREVICH E.V. THE MOLECULAR ACROBATICS OF ARRESTIN ACTIVATION (2004) 280 280

Development of Knowledge Bases

Technical description

In a co-cittion network, the strength of the relationship between a reference pair \(m\) and \(n\) (\(s_{m,n}^{coc}\)) is expressed by the number of publications \(C\) which are jointly citing reference \(m\) and \(n\).

\[s_{m,n}^{coc} = \sum_i c_{i,m} c_{i,n}\]

The intuition here is that references which are frequently cited together are likely to share commonalities in theory, topic, methodology, or context. It can be interpreted as a measure of similarity as evaluated by other researchers that decide to jointly cite both references. Because the publication process is time-consuming, co-citation is a backward-looking measure, which is appropriate to map the relationship between core literature of a field.

Research Areas: Bibliographic coupling analysis

Research Areas main summary

This is arguably the more interesting part. Here, we identify the literature’s current knowledge frontier by carrying out a bibliographic coupling analysis of the publications in our corpus. This measure uses bibliographical information of publications to establish a similarity relationship between them. Again, method details to be found in the tab Technical description. As you will see, we identify the main research area, but also a set of adjacent research areas with some theoretical/methodological/application overlap.

To identify communities in the field’s knowledge frontier (labeled research areas) we again use the Lovain Algorithm (Blondel et al., 2008). We identify the following communities = research areas.

label AU PY TI dgr_int TC TC_year
Research Area 1: RA 1: unlabeled (n = 1077, density =0.15)
RA 1: unlabeled KOH A;DE VADDER F;KOVA… 2016 FROM DIETARY FIBER TO HOST PHYSIOLOGY: SHORT-CHAIN FATTY ACIDS AS KEY BACTERIAL METABOLITES 3.34 2285 380.83
RA 1: unlabeled THURSBY E;JUGE N 2017 INTRODUCTION TO THE HUMAN GUT MICROBIOTA 5.11 995 199.00
RA 1: unlabeled SONNENBURG JL;BÄCKHED F 2016 DIET-MICROBIOTA INTERACTIONS AS MODERATORS OF HUMAN METABOLISM 4.15 1067 177.83
RA 1: unlabeled DESAI MS;SEEKATZ AM;KO… 2016 A DIETARY FIBER-DEPRIVED GUT MICROBIOTA DEGRADES THE COLONIC MUCUS BARRIER AND ENHANCES PATHOGEN SUSCEPTIBILITY 4.10 1077 179.50
RA 1: unlabeled ROOKS MG;GARRETT WS 2016 GUT MICROBIOTA, METABOLITES AND HOST IMMUNITY 2.85 1323 220.50
RA 1: unlabeled LEVY M;KOLODZIEJCZYK A… 2017 DYSBIOSIS AND THE IMMUNE SYSTEM 4.50 622 124.40
RA 1: unlabeled MAKKI K;DEEHAN EC;WALT… 2018 THE IMPACT OF DIETARY FIBER ON GUT MICROBIOTA IN HOST HEALTH AND DISEASE 3.25 804 201.00
RA 1: unlabeled THAISS CA;ZMORA N;LEVY… 2016 THE MICROBIOME AND INNATE IMMUNITY 2.37 927 154.50
RA 1: unlabeled BELKAID Y;HARRISON OJ 2017 HOMEOSTATIC IMMUNITY AND THE MICROBIOTA 4.36 495 99.00
RA 1: unlabeled BAÜMLER AJ;SPERANDIO V 2016 INTERACTIONS BETWEEN THE MICROBIOTA AND PATHOGENIC BACTERIA IN THE GUT 3.07 595 99.17
Research Area 2: RA 2: unlabeled (n = 580, density =0.33)
RA 2: unlabeled O’NEILL LAJ;KISHTON RJ… 2016 A GUIDE TO IMMUNOMETABOLISM FOR IMMUNOLOGISTS 2.40 1262 210.33
RA 2: unlabeled BUCK MD;SOWELL RT;KAEC… 2017 METABOLIC INSTRUCTION OF IMMUNITY 3.57 549 109.80
RA 2: unlabeled SUKUMAR M;LIU J;MEHTA … 2016 MITOCHONDRIAL MEMBRANE POTENTIAL IDENTIFIES CELLS WITH ENHANCED STEMNESS FOR CELLULAR THERAPY 6.69 201 33.50
RA 2: unlabeled KISHTON RJ;SUKUMAR M;R… 2017 METABOLIC REGULATION OF T CELL LONGEVITY AND FUNCTION IN TUMOR IMMUNOTHERAPY 5.28 199 39.80
RA 2: unlabeled JOHNSON MO;WOLF MM;MAD… 2018 DISTINCT REGULATION OF TH17 AND TH1 CELL DIFFERENTIATION BY GLUTAMINASE-DEPENDENT METABOLISM 3.86 243 60.75
RA 2: unlabeled LOFTUS RM;FINLAY DK 2016 IMMUNOMETABOLISM: CELLULAR METABOLISM TURNS IMMUNE REGULATOR 3.23 238 39.67
RA 2: unlabeled ALMEIDA L;LOCHNER M;BE… 2016 METABOLIC PATHWAYS IN T CELL ACTIVATION AND LINEAGE DIFFERENTIATION 2.98 217 36.17
RA 2: unlabeled NEWTON R;PRIYADHARSHIN… 2016 IMMUNOMETABOLISM OF REGULATORY T CELLS 3.24 196 32.67
RA 2: unlabeled MENK AV;SCHARPING NE;M… 2018 EARLY TCR SIGNALING INDUCES RAPID AEROBIC GLYCOLYSIS ENABLING DISTINCT ACUTE T CELL EFFECTOR FUNCTIONS 3.54 178 44.50
RA 2: unlabeled GERRIETS VA;KISHTON RJ… 2016 FOXP3 AND TOLL-LIKE RECEPTOR SIGNALING BALANCE T REG CELL ANABOLIC METABOLISM FOR SUPPRESSION 2.28 276 46.00
Research Area 3: RA 3: unlabeled (n = 462, density =0.81)
RA 3: unlabeled CHINEN T;KANNAN AK;LEV… 2016 AN ESSENTIAL ROLE FOR THE IL-2 RECEPTOR IN T REG CELL FUNCTION 7.08 393 65.50
RA 3: unlabeled KAMADA T;TOGASHI Y;TAY… 2019 PD-1+ REGULATORY T CELLS AMPLIFIED BY PD-1 BLOCKADE PROMOTE HYPERPROGRESSION OF CANCER 6.44 361 120.33
RA 3: unlabeled TOGASHI Y;SHITARA K;NI… 2019 REGULATORY T CELLS IN CANCER IMMUNOSUPPRESSION — IMPLICATIONS FOR ANTICANCER THERAPY 4.81 440 146.67
RA 3: unlabeled DOMINGUEZ-VILLAR M;HAF… 2018 REGULATORY T CELLS IN AUTOIMMUNE DISEASE 7.24 282 70.50
RA 3: unlabeled MAJ T;WANG W;CRESPO J;… 2017 OXIDATIVE STRESS CONTROLS REGULATORY T CELL APOPTOSIS AND SUPPRESSOR ACTIVITY AND PD-L1-BLOCKADE RESISTANCE IN TUMOR 5.27 341 68.20
RA 3: unlabeled LI MO;RUDENSKY AY 2016 T CELL RECEPTOR SIGNALLING IN THE CONTROL OF REGULATORY T CELL DIFFERENTIATION AND FUNCTION 6.37 269 44.83
RA 3: unlabeled WING JB;TANAKA A;SAKAG… 2019 HUMAN FOXP3 + REGULATORY T CELL HETEROGENEITY AND FUNCTION IN AUTOIMMUNITY AND CANCER 6.51 250 83.33
RA 3: unlabeled PLITAS G;RUDENSKY AY 2016 REGULATORY T CELLS: DIFFERENTIATION AND FUNCTION 10.96 142 23.67
RA 3: unlabeled TAKEUCHI Y;NISHIKAWA H 2016 ROLES OF REGULATORY T CELLS IN CANCER IMMUNITY 5.18 284 47.33
RA 3: unlabeled KITAGAWA Y;OHKURA N;KI… 2017 GUIDANCE OF REGULATORY T CELL DEVELOPMENT BY SATB1-DEPENDENT SUPER-ENHANCER ESTABLISHMENT 7.20 184 36.80
Research Area 4: RA 4: unlabeled (n = 462, density =0.45)
RA 4: unlabeled PAVLOVA NN;THOMPSON CB 2016 THE EMERGING HALLMARKS OF CANCER METABOLISM 3.16 2546 424.33
RA 4: unlabeled DUCKER GS;RABINOWITZ JD 2017 ONE-CARBON METABOLISM IN HEALTH AND DISEASE 5.55 738 147.60
RA 4: unlabeled DE BERARDINIS RJ;CHAND… 2016 FUNDAMENTALS OF CANCER METABOLISM 3.19 1281 213.50
RA 4: unlabeled VANDER HEIDEN MG;DEBER… 2017 UNDERSTANDING THE INTERSECTIONS BETWEEN METABOLISM AND CANCER BIOLOGY 3.80 981 196.20
RA 4: unlabeled YANG M;VOUSDEN KH 2016 SERINE AND ONE-CARBON METABOLISM IN CANCER 4.57 433 72.17
RA 4: unlabeled NEWMAN AC;MADDOCKS ODK 2017 ONE-CARBON METABOLISM IN CANCER 9.27 189 37.80
RA 4: unlabeled LUENGO A;GUI DY;VANDER… 2017 TARGETING METABOLISM FOR CANCER THERAPY 3.97 403 80.60
RA 4: unlabeled MATTAINI KR;SULLIVAN M… 2016 THE IMPORTANCE OF SERINE METABOLISM IN CANCER 7.48 186 31.00
RA 4: unlabeled MA EH;BANTUG G;GRISS T… 2017 SERINE IS AN ESSENTIAL METABOLITE FOR EFFECTOR T CELL EXPANSION 4.44 263 52.60
RA 4: unlabeled PACOLD ME;BRIMACOMBE K… 2016 A PHGDH INHIBITOR REVEALS COORDINATION OF SERINE SYNTHESIS AND ONE-CARBON UNIT FATE 4.06 250 41.67
Research Area 5: RA 5: unlabeled (n = 429, density =0.35)
RA 5: unlabeled SHAMJI MH;DURHAM SR 2017 MECHANISMS OF ALLERGEN IMMUNOTHERAPY FOR INHALED ALLERGENS AND PREDICTIVE BIOMARKERS 5.37 226 45.20
RA 5: unlabeled ROBERTS G;PFAAR O;AKDI… 2018 EAACI GUIDELINES ON ALLERGEN IMMUNOTHERAPY: ALLERGIC RHINOCONJUNCTIVITIS 3.95 297 74.25
RA 5: unlabeled SHAMJI MH;KAPPEN JH;AK… 2017 BIOMARKERS FOR MONITORING CLINICAL EFFICACY OF ALLERGEN IMMUNOTHERAPY FOR ALLERGIC RHINOCONJUNCTIVITIS AND ALLERGIC ASTHMA… 5.08 198 39.60
RA 5: unlabeled DEMOLY P;EMMINGER W;RE… 2016 EFFECTIVE TREATMENT OF HOUSE DUST MITE-INDUCED ALLERGIC RHINITIS WITH 2 DOSES OF THE SQ HDM SLIT-TABLET: RESULTS FROM A RA… 3.82 146 24.33
RA 5: unlabeled DURHAM SR;PENAGOS M 2016 SUBLINGUAL OR SUBCUTANEOUS IMMUNOTHERAPY FOR ALLERGIC RHINITIS? 5.32 100 16.67
RA 5: unlabeled VIRCHOW JC;BACKER V;KU… 2016 EFFICACY OF A HOUSE DUST MITE SUBLINGUAL ALLERGEN IMMUNOTHERAPY TABLET IN ADULTS WITH ALLERGIC ASTHMA: A RANDOMIZED CLINIC… 1.46 257 42.83
RA 5: unlabeled SCADDING GW;CALDERON M… 2017 EFFECT OF 2 YEARS OF TREATMENT WITH SUBLINGUAL GRASS POLLEN IMMUNOTHERAPY ON NASAL RESPONSE TO ALLERGEN CHALLENGE AT 3 YEA… 2.99 124 24.80
RA 5: unlabeled JUTEL M;AGACHE I;BONIN… 2016 INTERNATIONAL CONSENSUS ON ALLERGEN IMMUNOTHERAPY II: MECHANISMS, STANDARDIZATION, AND PHARMACOECONOMICS 2.26 155 25.83
RA 5: unlabeled DHAMI S;NURMATOV U;ARA… 2017 ALLERGEN IMMUNOTHERAPY FOR ALLERGIC RHINOCONJUNCTIVITIS: A SYSTEMATIC REVIEW AND META-ANALYSIS 1.89 167 33.40
RA 5: unlabeled NOLTE H;BERNSTEIN DI;N… 2016 EFFICACY OF HOUSE DUST MITE SUBLINGUAL IMMUNOTHERAPY TABLET IN NORTH AMERICAN ADOLESCENTS AND ADULTS IN A RANDOMIZED, PLAC… 3.13 94 15.67
Research Area 6: RA 6: unlabeled (n = 348, density =0.3)
RA 6: unlabeled HUGHES CE;NIBBS RJB 2018 A GUIDE TO CHEMOKINES AND THEIR RECEPTORS 1.61 345 86.25
RA 6: unlabeled JANSSENS R;STRUYF S;PR… 2018 THE UNIQUE STRUCTURAL AND FUNCTIONAL FEATURES OF CXCL12 2.98 129 32.25
RA 6: unlabeled POZZOBON T;GOLDONI G;V… 2016 CXCR4 SIGNALING IN HEALTH AND DISEASE 3.04 124 20.67
RA 6: unlabeled BONECCHI R;GRAHAM GJ 2016 ATYPICAL CHEMOKINE RECEPTORS AND THEIR ROLES IN THE RESOLUTION OF THE INFLAMMATORY RESPONSE 2.76 89 14.83
RA 6: unlabeled STONE MJ;HAYWARD JA;HU… 2017 MECHANISMS OF REGULATION OF THE CHEMOKINE-RECEPTOR NETWORK 1.24 141 28.20
RA 6: unlabeled GIRBL T;LENN T;PEREZ L… 2018 DISTINCT COMPARTMENTALIZATION OF THE CHEMOKINES CXCL1 AND CXCL2 AND THE ATYPICAL RECEPTOR ACKR1 DETERMINE DISCRETE STAGES … 1.20 127 31.75
RA 6: unlabeled MASSARA M;BONAVITA O;M… 2016 ATYPICAL CHEMOKINE RECEPTORS IN CANCER: FRIENDS OR FOES? 2.51 54 9.00
RA 6: unlabeled HAO H;HU S;CHEN H;BU D… 2017 LOSS OF ENDOTHELIAL CXCR7 IMPAIRS VASCULAR HOMEOSTASIS AND CARDIAC REMODELING AFTER MYOCARDIAL INFARCTION: IMPLICATIONS FO… 2.32 56 11.20
RA 6: unlabeled SZPAKOWSKA M;NEVINS AM… 2018 DIFFERENT CONTRIBUTIONS OF CHEMOKINE N-TERMINAL FEATURES ATTEST TO A DIFFERENT LIGAND BINDING MODE AND A BIAS TOWARDS ACTI… 3.89 33 8.25
RA 6: unlabeled CHENG X;WANG H;ZHANG X… 2017 THE ROLE OF SDF-1/CXCR4/CXCR7 IN NEURONAL REGENERATION AFTER CEREBRAL ISCHEMIA 2.03 62 12.40
Research Area 7: RA 7: unlabeled (n = 311, density =0.42)
RA 7: unlabeled VIVIER E;ARTIS D;COLON… 2018 INNATE LYMPHOID CELLS: 10 YEARS ON 3.97 854 213.50
RA 7: unlabeled HABER AL;BITON M;ROGEL… 2017 A SINGLE-CELL SURVEY OF THE SMALL INTESTINAL EPITHELIUM 0.93 632 126.40
RA 7: unlabeled COLONNA M 2018 INNATE LYMPHOID CELLS: DIVERSITY, PLASTICITY, AND UNIQUE FUNCTIONS IN IMMUNITY 2.82 176 44.00
RA 7: unlabeled EBBO M;CRINIER A;VÉLY … 2017 INNATE LYMPHOID CELLS: MAJOR PLAYERS IN INFLAMMATORY DISEASES 1.83 194 38.80
RA 7: unlabeled KABATA H;MORO K;KOYASU S 2018 THE GROUP 2 INNATE LYMPHOID CELL (ILC2) REGULATORY NETWORK AND ITS UNDERLYING MECHANISMS 2.91 117 29.25
RA 7: unlabeled MORITA H;KUBO T;RÜCKER… 2019 INDUCTION OF HUMAN REGULATORY INNATE LYMPHOID CELLS FROM GROUP 2 INNATE LYMPHOID CELLS BY RETINOIC ACID 3.69 86 28.67
RA 7: unlabeled BAL SM;GOLEBSKI K;SPITS H 2020 PLASTICITY OF INNATE LYMPHOID CELL SUBSETS 2.62 111 55.50
RA 7: unlabeled PANDA SK;COLONNA M 2019 INNATE LYMPHOID CELLS IN MUCOSAL IMMUNITY 3.01 94 31.33
RA 7: unlabeled CORTEZ VS;ULLAND TK;CE… 2017 SMAD4 IMPEDES THE CONVERSION OF NK CELLS INTO ILC1-LIKE CELLS BY CURTAILING NON-CANONICAL TGF-Β SIGNALING 1.32 182 36.40
RA 7: unlabeled GURRAM RK;ZHU J 2019 ORCHESTRATION BETWEEN ILC2S AND TH2 CELLS IN SHAPING TYPE 2 IMMUNE RESPONSES 3.53 66 22.00
Research Area 8: RA 8: unlabeled (n = 236, density =0.27)
RA 8: unlabeled WACKER D;STEVENS RC;RO… 2017 HOW LIGANDS ILLUMINATE GPCR MOLECULAR PHARMACOLOGY 1.17 281 56.20
RA 8: unlabeled SMITH JS;LEFKOWITZ RJ;… 2018 BIASED SIGNALLING: FROM SIMPLE SWITCHES TO ALLOSTERIC MICROPROCESSORS 0.71 327 81.75
RA 8: unlabeled WACKER D;WANG S;MCCORV… 2017 CRYSTAL STRUCTURE OF AN LSD-BOUND HUMAN SEROTONIN RECEPTOR 1.13 202 40.40
RA 8: unlabeled INOUE A;RAIMONDI F;KAD… 2019 ILLUMINATING G-PROTEIN-COUPLING SELECTIVITY OF GPCRS 1.10 171 57.00
RA 8: unlabeled GUREVICH VV;GUREVICH EV 2019 GPCR SIGNALING REGULATION: THE ROLE OF GRKS AND ARRESTINS 1.02 182 60.67
RA 8: unlabeled KRISHNA KUMAR K;SHALEV… 2019 STRUCTURE OF A SIGNALING CANNABINOID RECEPTOR 1-G PROTEIN COMPLEX 0.91 189 63.00
RA 8: unlabeled VALENTINO RJ;VOLKOW ND 2018 UNTANGLING THE COMPLEXITY OF OPIOID RECEPTOR FUNCTION 1.15 115 28.75
RA 8: unlabeled CONIBEAR AE;KELLY E 2019 A BIASED VIEW OF Μ-OPIOID RECEPTORS? 2.35 54 18.00
RA 8: unlabeled STAUS DP;HU H;ROBERTSO… 2020 STRUCTURE OF THE M2 MUSCARINIC RECEPTOR–Β-ARRESTIN COMPLEX IN A LIPID NANODISC 1.03 121 60.50
RA 8: unlabeled KIM K;CHE T;PANOVA O;D… 2020 STRUCTURE OF A HALLUCINOGEN-ACTIVATED GQ-COUPLED 5-HT2A SEROTONIN RECEPTOR 1.05 100 50.00

Development

Connectivity between the research areas

Technical description

In a bibliographic coupling network, the coupling-strength between publications is determined by the number of commonly cited references they share, assuming a common pool of references to indicate similarity in context, methods, or theory. Formally, the strength of the relationship between a publication pair \(i\) and \(j\) (\(s_{i,j}^{bib}\)) is expressed by the number of commonly cited references.

\[s_{i,j}^{bib} = \sum_m c_{i,m} c_{j,m}\]

Since our corpus contains publications which differ strongly in terms of the number of cited references, we normalize the coupling strength by the Jaccard similarity coefficient. Here, we weight the intercept of two publications’ bibliography (shared refeences) by their union (number of all references cited by either \(i\) or \(j\)). It is bounded between zero and one, where one indicates the two publications to have an identical bibliography, and zero that they do not share any cited reference. Thereby, we prevent publications from having high coupling strength due to a large bibliography (e.g., literature surveys).

\[S_{i,j}^{jac-bib} =\frac{C(i \cap j)}{C(i \cup j)} = \frac{s_{i,j}^{bib}}{c_i + c_j - s_{i,j}^{bib}}\]

More recent articles have a higher pool of possible references to co-cite to, hence they are more likely to be coupled. Consequently, bibliographic coupling represents a forward looking measure, and the method of choice to identify the current knowledge frontier at the point of analysis.

Knowledge Bases, Research Areas & Topics Interaction

Endnotes

All results are preliminary so far…